What was once here, is now gone
by Electricprincess889
Summary: This story is at twist on the events after what happened on ALtomare. What happens when Ash returns three years later? Will old feelings coome to the surface and what happens when all his traveling companios come along? Unova has not taken place yet
1. Chapter 1

What was once here, is now gone Chapter one

Disclaimer: I do not own Pokémon. All rights go to Nintendo. (Insert more legal stuff here.)

Authors note: Hello to all readers in fanfiction world. I thank you for taking your time to stop and read my fanfiction. I would appreciate it if you would review and leave constructive criticism only. That will help me make the story better. This is also my first Pokémon fanfiction .So please bear with me. Please don't flame too badly! Now on to the first chapter!

"Speech"

'Telepathy'

'_Thoughts'_

Chapter one

Flashback

There was a huge tidal wave and it was heading towards the island city of Altomare. A wall of pure destruction that showed no sign of stopping its chaotic path. Out of nowhere, a red and white dragon- like creature raced towards the wave in an effort to save the doomed island. She was followed by an almost identical dragon. The second dragon was blue and white and was slightly bigger than the first. As the dragons started to focus their power, their bodies glowed with an unearthly light. As they raced towards the wave, they could hear behind them cries of panic and sadness. There was one voice that stood out more than all the other to the red and white dragon. She looked behind her and her heart broke almost immediately. A boy about eleven years old wearing a black t-shirt, jeans and had eyes that were almost black, with untamable black hair had a look of such sadness that the red and white dragon almost turned around to fly to the boy's side. The one thing that stopped her from doing so was the threat that was about to destroy her home. And for the sake of keeping the boy and the rest of her family alive, she had to do what needed to be done. The two dragons continued on their path towards the tidal wave. The pair crashed into the wave with such a force that could challenge the power of the creator, Mew. The wave disappeared almost instantly. After a few moments, the water started to return to the silent city. The only thing that could be seen in the water was the red and white dragon. The blue and white dragon was nowhere to be seen.

End Flashback

Latias woke up drenched in a cold sweat. "The Nightmare" as she like to call it, had once again run its weekly course. Not only did it terrify her, but when she was having it, nothing could make her get up or become active until it was done. The worst part about it was that "The Nightmare" wasn't really a nightmare. It was a memory. In reality, the red and white dragon was her and the blue and white dragon used to be her brother Latios. Even three years after he had become the new soul dew, the memory still refused to leave her. What made the nightmare worse today was that today was third year anniversary of Latios' death. Even though it was as selfish as it sounded, there was one good thing that came out of Latios' passing. The first time she had met Ash, he had been, of course, in a form of trouble. He had been heading head first towards a concrete wall. Before Latias could become lost in the past again, Bianca opened the door to the room that she had been lending to Latias. When Bianca opened the door, Latias realized it was about midday. Since her experience with the Team Rocket agents, Latias was a lot more distrusting of people. She almost turned invisible but resisted the urge to.

"Good Morning Latias! Even though today is not the best day, I have something that we are going to do that I think you will enjoy," Bianca said.

Latias jumped out of the bed and pinned Bianca to the floor. After Latios had died, Latias gained most of Latios' unused abilities. She was able to use telepathy and was able to keep her human form while she slept to name a few.

"Tell me! Tell me! Tell me,' Latias squealed in her mind and in Bianca's.

With only one guardian left in the city, Latias had to become stronger then she already was to defend the city when it was needed.

Bianca grinned," I'm going to help you change your human appearance!"

Bianca laughed at Latias' confused expression.

"Since you have used my form for so long, you are starting to act like me and not act like you used to" Bianca explained.

'Is that a bad thing?' Latias looked hurt. She thought that Bianca liked that Latias looked like her.

"Not really, but you should have a personality that you can call your own and a form that no one else has"

**Well the first chapter is done. Let me know what everyone thinks and who should be on Ash's Pokémon team besides a Gyarados and Pikachu. No Pokémon from Unova. He can have ****one**** legendary. Thank you for reading and remember to review! **


	2. Chapter 2

**Author's note: Thanks to all of the people who reviewed my last chapter. I was really happy to get feedback so quickly after I posted the story. I love all the encouraging words that you have for me. And now on with the chapter! **

_Last time….._

_Bianca ginned," I'm going to help you change your human appearance!"_

_Bianca laughed at Latias' confused expression._

"_Since you have used my form for so long, you are starting to act like me and not act like you used to" Bianca explained._

'_Is that a bad thing?' Latias looked hurt. She thought that Bianca liked that Latias looked like her._

"_Not really, you should have a personality that you can call your own and a form that no one else has."_

What was one here, is now gone Chapter two

Disclaimer: I do not own Pokémon. All rights go to Nintendo. Insert more legal stuff here.

Chapter two

At the same time…..

A boat was sailing toward the small island city of Altomare. A young man, about the age of fourteen, was completely oblivious to his surroundings. He was staring intently at the horizon thinking about his latest defeat. He was looking around so hard, one because he was trying to get a glimpse of the island he had longed to return to for the past three years and two because he was trying to figure out what he had done wrong during the Lily of the Valley conference. He had come so close to winning yet had been do far away. Seeing the Latios that Tobias had brought back some painful memories to Ash's mind from several years earlier. While Ash was yelling at himself internally, Brock came up to the deck from his room below the ship. He noticed that Ash had a look of absolute pain on his face. Ash had never told anyone but while they were on their way to save Pikachu at the Tree of Beginning, Sir Aaron's Lucario recognized what a powerful aura Ash had and forced him to train in the ways of aura to prevent the knowledge of how to use aura to fade away and be lost forever. Ash felt so guilty that he let his pokemon down once again was using his aura to hurt himself on the inside. He was trying to make up for all of the hyper beams, giga impacts and takedown attacks that his pokemon endured for him. But also in a way he was healing himself to symbolize all the healing that he did for them. Brock walked up to Ash and lightly tapped Ash on the shoulder to gain his attention. Ash flinched violently as if Brock's touch had hurt him. The only attention that Brock gained from Ash was that he looked at Brock out of the corner of his eyes, shrugged Brock's hand off of his shoulder and turned back to look at the sea. Brock tried to keep a straight face and not look like Ash's gesture ad hurt him but it was hard. Ever since they had left Altomare all those years ago, Ash never spoke a word as if he blamed Latios' death on himself and acted like he could have prevented it. Brock had no idea how Ash was able to communicate or give commands to his pokemon on the battlefield but Ash was able to somehow. That gave Ash the element of surprise because his opponents would not be expecting what the attacks would be. But it also hurt Brock to see the once lively kid turn in to a shadow of his former self.

"Ash, it's okay to be upset that you didn't win, but you can't keeping beating yourself down and hurting yourself over one loss. I really wish you would talk to me and tell me what's wrong and how I can help you." Brock looked at Ash sadly.

Ash looked at Brock out of the corner of his eye again and stood up from where he had been leaning on the rail of the ship. When he stood up straight, Ash was about as tall as Brock. Ash looked Brock directly in the eyes and Brock could see all the pain and sorrow Ash had been holding in since they had left Altomare.

The door leading down towards the rooms below the deck opened. Dawn, Max, May and Misty had come along on the trip to the island to see the place that had caused Ash to become mute. Misty had already been to Altomare but had come along to revisit some places and try to prove to Ash that there was more to life then living in the past. Misty also had some secret motive to gain Ash for herself but tried to hide them. May had come to Altomare because after they visited the island, she planned to try contests in the Kanto region. Like Misty, May had hidden motives for coming along besides competing in Kanto. Dawn came along with Ash and Brock because she had nothing better to do. She too wanted Ash for herself, though in her mind, Ash would want to date a girl three years younger than him **(A/N Sorry to burst your bubble Dawn, but not all men are like that)**. Max had purely come along because they were going to an island that was known to have the legendary Eon twin dragons as guardians of the city. Brock hadn't had the heart to tell Max that one of the twins was dead. The four off them had been listening to Brock's almost one-sided conversation through the door leading down below the deck of the ship.

Max ran over to try and comfort Ash about his defeat. Like Brock said Ash, you can't let yourself get down about one defeat. Try and cheer up, we're going to an island where there are legendary pokemon! We might get lucky and see them."

This did nothing to boost Ash's confidence. Ash slowly began to pry Max off of his shirt from where Max had been gripping it tightly as if Max was going to try and shake some sense into Ash. The three girls hung back to let the boys try and get through to Ash. They would try later on when they were alone with Ash in maybe a secluded romantic spot in the city. Before they had come up onto the deck, the girls had, had a really long debate about who Ash really loved. That was one of the reasons that Brock had come up on the deck in the first place. The girls had forced Brock to listen to their debate about who Ash loved for HOURS! For all Brock knew, Ash was oblivious to the feelings of the three girls. But after he became mute, Ash became a lot more observant of his surroundings and wasn't as clueless as everyone thought.

Ash turned suddenly to stare back out at the sea again. A smile tugged at the corner of his mouth. He could see Altomare in the distance, getting closer with each passing minute. Ash closed his eyes and silently sent out his aura to scan the shoreline. His vision turned a light blue with a hint of silver in the outline to show what a pure heart Ash had. Each person on the shore had a distinct color that showed how good or bad their heart was. Ash sighed with disappointment; Latias was not at the shore. Not that he expected her to be, he hadn't told her that he was coming back to the island. But Ash had to check, even though he knew what he was going to find. Ash slowly turned around to see his friend's confused faces. Brock looked at Ash with understanding in his eyes but Misty looked angry. She was upset at the thought that Ash would be that enthusiastic about seeing a certain red and white dragon. Misty stormed over to Ash and proceeded to try and hurt Ash without saying a word to her other companions. As she tried to punch/slap him, Ash ducked and safely moved to the other side of the ship, where he turned to stare out at the city again trying to sense Latias. He sighed and opened his eyes again; he still could not sense Latias anywhere close to the shoreline. Behind Ash all of his friends looked utterly confused at what had just happened but Brock and Misty. Luckily for Ash the boat docked at the harbor at that moment. The horrible thing about that was that Misty now stood between Ash and the dock. And Misty had made no move to disembark off of the ship with all of the other passengers. Ash looked at Misty, who was slowly advancing on him, and the water. Ash made a spilt second decision and pulled out one of his poke balls.

Ash calmly turned his back towards Misty and sent out a huge shiny Gyarados. Misty's mouth fell open, the Gyarados was way better than the ones she had trained. Even for it being a shiny, the color was like looking into a moving pool of bright red and orange lava. Misty had no idea that Ash owned a Gyarados, let alone a shiny one. Ash jumped on the water-types back and made a beeline for the shore. Moments later he was standing a small distance away from where his friends were standing on the shore.

Ash calmly returned the water-type and prepared himself for what was going to end up being Misty screaming at Ash and attempting to hit him. Misty soon rushed toward the group and attempted to smack Ash on the head. Ash, once again, ducked and moved a safe distance away from Misty. He turned his back to the group once again and sent out his aura to find the fastest way to get to the secret garden. Brock, Max, May and Dawn looked amazed at Ash. He had pretty much ignored Misty and the rest of the group and was doing what he had been doing for most of the two day boat ride.

Ash, with his eyes still closed moved out of the way of Misty's fist as she attempted to hit him from behind. Ash's eyes shot open as he thought he detected a familiar aura in the city. He motioned to Pikachu to follow him and they both ran off towards an unknown place.

"Ash come back here! You're going to get lost again!" Dawn yelled after Ash.

"Don't worry about Ash, Dawn. Ash, Misty and I have been to Altomare before. Ash knows his way around the city pretty well. But just in case, Misty, I want you to take Max, May and Dawn to the pokemon center and get us checked in for a couple of nights." Brock said without taking his eyes off of Ash's retreating form. "I'm going to follow Ash to make sure he is all right and doesn't get lost o badly."

'Was it really necessary to just run off like that?' Pikachu looked at his trainer long and hard. 'You don't have to make it that obvious that you want to see Latias.'

'Yes Pikachu, it was and you know it. If we had stayed any longer, Misty would have eventually found a way to pound my face into the dust.' Ash shot back just as quickly.

'Just try not to get us lost like you did last time we were here.' Pikachu was referring to the time when they had first met Latias and she had led them through a chase around the city. It had taken them hours to find their way back to the pokemon center.

Ash rolled his eyes, 'You have no faith in my sense of direction. You're starting to act like all the other people in our group of friends. All those times we had gotten lost in Sinnoh and Hoenn were not my fault. It's not like they follow the way I suggest we go. This then turns out to be the way we actually needed to go in the first place.' Ash pointed out. 'Besides I've been to Altomare before. I know where I am going this time.'

As Ash thought this, they arrived in the square where they had first met Latias. 'All that we have to do now is to sit and wait. I know she felt us as soon as we stepped foot on the island.'

**Author's note: And that is the end of chapter two. Thank you again to all of the people who reviewed my last chapter. I have decided on all of Ash's team except the legendary. Thank you for reading and remember to review! **


	3. Chapter 3

Chapter 3

Disclaimer: I do not own the pokemon games or series. All rights go to Nintendo. Insert more legal stuff here

**Author's note: Thank you to all of the people who reviewed my last two chapters. I'm happy to know that I have people who read what I write and have only good things to say. Now on to the third chapter (Ash's team has been decided. His team will come play in later chapters)**

_Last time… _

'_Was it really necessary to just run off like that?' Pikachu looked at his trainer long and hard. 'You don't have to make it that obvious that you want to see Latias.'_

'_Yes Pikachu, it was and you know it. If we had stayed any longer, Misty would have eventually found a way to pound my face into the dust.' Ash shot back just as quickly. _

'_Just try not to get us lost like you did last time we were here.' Pikachu was referring to the time when they had first met Latias and she had led them through a chase around the city. It had taken them hours to find their way back to the pokemon center. _

_Ash rolled his eyes, 'You have no faith in my sense of direction. You're starting to act like all the other people in our group of friends. All those times we had gotten lost in Sinnoh and Hoenn were not my fault. It's not like they follow the way I suggest we go. This then turns out to be the way we actually needed to go in the first place.' Ash pointed out. 'Besides I've been to Altomare before. I know where I am going this time.'_

_As Ash thought this, they arrived in the square where they had first met Latias. 'All that we have to do now is to sit and wait. I know she felt us as soon as we stepped foot on the island.'_

"Speech"

'Telepathy'

'_Thoughts'_

'Are we done yet?' Latias whined. 'Bianca, you have been having me change my form for the past 12 hours!' Latias continued to whine some more.

"Don't exaggerate Latias! You've only been doing this for about an hour." Bianca said while glancing down at her watch. "Besides," Bianca continued, "I think I have got the perfect appearance for you Latias! Just follow what's on the drawing pad."

Latias studied the notebook for a moment and nodded. She closed her eyes and her figure started to glow. The glow faded, Bianca took one look at Latias and gasped. 'What's wrong?' Latias said with a frown. Bianca just silently turned Latias around to face the mirror that was in Bianca's room. Latias took one look at her new form and her mouth fell open in surprise. Latias now had shoulder length wavy red hair, green eyes and a light golden glow to her skin. She was wearing a red shirt, with a green and blue skirt and white shoes**. (A/N When I was designing the outfit, I tried to incorporate all of the Lati's colors. Red for Latias, blue for Latios, green for Bianca and the white shoes have a connection to all of them. Not that Bianca is a Lati.)**

'Wow Bianca! You really outdid yourself this time.' Latias thought. Bianca put her hand behind her head and blushed. "It was the least I could do Latias" A blushing Bianca said. 'Let's go show Lo-.' Latias coked her head to the side as if she was listening to something.

Bianca looked at Latias with a worried face," What is it Latias? Do you sense something? Is the city in danger" Bianca asked in rapid fire. Latias' mouth dropped open. Her face turned to an expression of surprise to one of pure joy. Bianca looked at Latias with curiosity in her eyes. "Latias….Is anything wrong?" Bianca asked hesitantly, "Is there anything that I can do to help?"

Latias spun around and started to demand answers from Bianca. 'Why didn't you tell me that he was coming back to Altomare? Did you really think that I wouldn't be able to tell when he came back?'

Bianca's expression hardened, "No Latias, I didn't. But I tried to keep it from you as long as I could. Ash is not the same any more Latias. He isn't the same trainer he used to be. Latios' death tore him apart and scattered the pieces to the wind. Things have changed Latias, it's time to get over your childish crush and face the facts. Nothing will be the same between you and Ash again"

Latias matched Bianca's cold voice with her own. 'Do you really think that I didn't know what happened to Ash? Did you really think that I would give up on him so easily?'

Latias paused to study Bianca's shocked expression. Latias had never spoken to anyone in that tone of voice. Not even when she was really angry. Bianca gulped as she felt the weight of what she had said to Latias in the heat of the moment come crashing down. And now she had to pay the price.

'If you thought I would, then you are wrong. So wrong Bianca. He still is the same Ash on the inside. He still is the same way to me. And once he sees me, everything will change.' Latias turned and ran out of the room after she let her final words sink into Bianca's mind. A tear slipped down Bianca's cheek as she realized something horrible. Latias would never act the same way towards Bianca again. Bianca had lost her lifelong friend. And maybe for good.

Latias ran through the streets and alleyways of Altomare. She was thrilled to finally have Ash back on the island after so many years it made her feel like she was going to burst from happiness. The only thing that diminished her happiness was about what happened with Bianca. Latias shook her head as she ran towards where she had last sensed Ash. It wasn't good to be thinking about negative things when having Ash back was such a wonderful thing. Latias had meant what she had said when she said that she knew what had happened to Ash and how she could help him. Unknown to Bianca and Lorenzo, Latias had left Altomare a lot to see Ash and observe him without him knowing. **(A/N Latias was not around when the group was at the Tree of Beginning). **

Latias slowly peeked her head around the corner and felt her heart skip a beat. Even from so far away, Latias could still feel Ash's pure aura radiating around him. There he was, sitting in the same square when they had first met while Latias was in her human form. Ash was sitting with his legs crossed, his head leaning back on the wall behind him, and had his eyes closed as if he was meditating. **(A/N Imagine Ash wearing what he did in the Sinnoh league). **'You can come out from behind the wall now.' A voice spoke suddenly in Latias' mind. Latias jumped and looked more closely at Ash. It didn't look like Ash had moved at all, so Latias didn't think that the voice was Ash's. Besides, Ash didn't have psychic powers, and he wasn't an Aura Guardian to begin with…Right? **(A/N Latias didn't know how wrong she was.). **

Latias heard the voice again, 'Really Latias! There is more to me then you might know. So can you please come out from behind the wall and sit next to me on the bench.' Yup, the voice defiantly sounded like Ash.Latias slowly turned the corner and went and sat down next to Ash. He opened one of his eyes to make sure Latias was there, and Ash's mouth almost fell open as he gazed at Latias' new form. Ash managed to keep his composure and closed his eyes again. 'You know,' he suddenly said, 'You leave the island a lot don't you Latias?' The dragoness almost fell off of the bench in surprise at what Ash 'said'.

'How did you now that I wasn't always on Altomare?' Latias said with confusion evident in her voice.

Ash chuckled much to Latias' confusion. It wasn't so much that Ash was laughing at her confusion; it was how he did it. Ash did the exact same thing that Latias does while she was in her form, he made the motions as if he was laughing but no sound came out of his mouth. That is what a normal person would see and hear. But for a telepathic pokemon like Latias, she could hear the sound of his laughter in her head. 'I know you leave the island to observe my group of friends,' Ash was able to say once he stopped laughing, 'I can tell because I could sense that you were there even though my friends couldn't.'

Confusion became one of the main emotions on Latias' face. 'How could you? I disguised my psychic energy so no one would try and capture me.' Latias stated in an "I know what I'm talking about so don't question me" telepathic tone of voice. Ash once again started to laugh much to her confusion. Once again. **(A/N Latias seems to get confused a lot. But you will understand why in later chapters). **

Ash calmed down enough to give Latias an answer. "What you didn't disguise was your aura,' Ash said in the same telepathic tone of voice Latias had just used. The dragoness just sat there staring at Ash with her mouth hanging open.

**And that is the conclusion of the third chapter. Thank you to all my readers who have been waiting a while to read this next chapter. I was having a bit of a writer's block and my schedule has been a bit overloaded anyways. So please read and review and I will try and get the next chapter up as soon as possible! Thanks for reading! **


	4. Chapter 4

What was once here is now gone a pokemon fanfiction chapter four

Disclaimer: I do not own pokemon, all rights go to Nintendo. Insert more legal stuff here.

**Thank you to everyone who reviewed my last chapter! If you want to read a good Altoshipping and aura story, I recommend that you read a fanfiction called Guardian of Altomare. I have read it several times and still love the plot. Now enough of my rambling, please enjoy the fourth, excuse me, third chapter of What was once here is now gone. **

"Speech"

'Telepathy'

'_Thoughts'_

Back with Brock….

Brock was absolutely amazed. After he had sent Max, May, and Dawn back to the pokemon center, Brock had been expecting Ash to find Latias immediately after returning to the island. Or to return to the Garden of the Lati. Instead Brock had found Ash sitting in a seemingly random square with a bench and a water pump.

Brock had found Ash sitting with his legs crossed, eyes closed, and his head leaning back against the wall like he would do when he was meditating. Brock was about to give Ash an earful of scolding for running off like that without saying anything…. Figuratively.

So, as Brock was about to make his way around the corner to scold Ash, a drop dead gorgeous girl poked her head around a different corner to look at Ash. Brocks saw her jump randomly and look around in surprise as if the girl had heard something that startled her. She then did something even more random and strange. She cocked her head to the side as if she was listening to someone or something speak to her.

The red headed girl walked hesitantly over to where Ash was sitting on the bench and proceeded to sit down next to him. Ash opened his eyes and gazed at the girl for a minute and the closed his eyes again. They began to, what seemed to Brock, have a silent conversation with each other. At one point in said silent conversation, the red head almost fell off of the bench in surprise at what Ash "said" to her. The girl stood up and stood in a stance in what Brock translated as, "I know what I am talking about so don't question me."

What surprised Brock even more was that Ash started to laugh. The funny part about that was that Brock couldn't hear any sound coming out of Ash's mouth. What was even stranger was that Ash hadn't laughed since they had left the island. After a few minutes of silently laughing, Ash calmed down enough so he could adopt a similar position like the one that the girl had just used.

Brock was shocked, again. In all of the years Brock had known Ash, he would never act that way towards a girl. When Brock and the rest of the group was around, Ash seemed to act like a completely dense idiot. But then again, Ash always acted that way around just about anyone. Again, Brock and the rest of the group had no idea how smart and observant Ash really was.

Brock was about to go confront the pair about how they were acting, when Misty finally caught up to Brock. "Geez Brock! Could you have slowed down just a little bit so a delicate girl like me could keep up?"**(A/N Misty delicate? I don't think so!).** Before Misty could say or do anything else that could give away their hiding place, Brock pulled Misty in to the shadow around the corner.

After Brock did so, he almostimmediately regretted his actions. Misty looked like she was about to hit him. "What do you think you are doing you pervert!" **(A/N Sorry couldn't resist taking a jab a Brock's over affectionate ways towards women). **Brock rolled his eyes at her and gestured for her to be quiet. He then pointed over at Ash and the girl who were still sitting in the square in the exact same place they had been in before, except that the girl was now sitting down with her hand on Ash's shoulder. Ash in turn was staring down at his lap looking like he was trying to fight back tears.

Misty's mouth dropped open, "…Brock….." Misty stopped to regain what little composure she had. "Who is that girl?" Brock swallowed nervously. When Misty started to use a deadly calm voice, it meant absolute pain and suffering for whoever her anger was directed at.

"I'm not really sure Misty," Brock managed to say after some time had passed. "When I found Ash, he was sitting in this square like he was meditating, like he normally does when he wants to be left alone. When I was going to go scold him for running off, that girl arrived and they have been having what I think is a telepathic conversation. Like the kind aura users and psychics can have."

Misty looked at Ash and began to laugh quietly. "I don't understand Misty, what's so funny?" Misty stopped laughing at Brock's confused expression. "What's funny is that Ash couldn't possibly have psychic powers, and he defiantly doesn't have the guts to be an Aura Guardian. Now if you can excuse me, I have some business to take care of." And with those words, Misty turned and began to march into the square where Ash and the girl were sitting.

Brock felt his jaw drop at Misty's stupidity. If Ash really was a psychic or an Aura Guardian, Ash wouldn't hesitate to do something to someone if he considered them to be interrupting something very personal. There had been a few times when they had been traveling in the Sinnoh region and the group had interrupted Ash when he was doing something important or when he wanted to be by himself and Ash had almost lost control, he would end up storming away in anger and the group would have to walk really fast to try and catch up with Ash. Meaning Brock would think he could see Ash's eyes flash blue for a minute but would always dismiss it as a trick of the light.

"Misty," Brock warned, "If you disturb Ash now, you will end up doing something that you will regret later."

Misty just brushed off Brock's warning and continued on her path towards the pair. "Whatever Brock, I think that I can handle Ash and some puny island girl by myself. They are just way to comfortable with each other to have just met randomly on the street."

And with those words, Brock watched Misty walk over to her doom. Along with what would be a lot of pain and suffering. Brock just didn't know who would receive it.

**Yay! I'm happy that I have gotten this chapter done so quickly. Remember to review!**


	5. Chapter 5

What was once here, is now gone a pokemon fanfiction chapter 5

Disclaimer: I do not own pokemon, all rights go to Nintendo. Insert more legal stuff here so I don't get sued.

**A/N I really do apologize for not updating in forever. Thank you for reviewing the last chapter. Now onto the next.**

'Telepathy'

"Speech"

'_Thoughts'_

With Ash and Latias, at the same time of Brock and Misty's conversation.

Latias looked at Ash for a long and hard moment. She was still trying to comprehend the story about the tree of beginning Ash had just told her. She glanced momentarily away and looked back at Ash's once cheerful face. He was looking down at his lap. Tears silently streaking down his cheeks and falling into his lap with almost an eerie silence that was unnatural. As she gazed at his tears, Latias noted that he had infused them with aura, liked he didn't want to be caught crying. Latias rolled her eyes slightly at that, Men, *sigh* always going on about how unmanly it is to cry in public.

With every tear that Ash shed for the loss of his friend, Latias was painfully reminded about Latios' death and how it affected Ash. What shocked Latias most about Ash's story, was that Ash was going to begin to open up to his friends about what he went through on Altomare. That is what hit her the hardest, He was going to speak again to his friends, but he had been shocked once more into his guilt ridden, non- speaking state of mind.

As Latias gazed at Ash, unsure of what to say to him to help him, the object of her attention suddenly snapped his head up and glanced toward the alleyway he had come from. He looked back at Latias, 'Remember Misty, Latias? Before she answered his question, Latias silently noted that his tears had vanished in an instant.

'Yes, Ash I do remember Misty. She was the annoying red headed girl that was always trying to get your attention while you were here… But what does she have to do with anything? I didn't think that much of her except that she got mad at you a lot and would start yelling at you about a bike every so often'

Ash gave a slight grin at Latias' analysis of Misty and her personality. Latias hadn't even spent that much time Misty and she had already gotten a 100% accurate description of her. He rolled his eyes at her comment and continued, 'Yes, well, Misty seems to think that I am "hers" and that I "belong" to her. And that she has every right to me since she happened to be my first traveling companion. Then again, May and Dawn also seem to think that I "belong" to them.'

Latias blinked slowly at Ash, trying her hardest not to laugh at the stupidity of Ash female traveling companions. They really thought they knew the real Ash, didn't they? If they knew the real Ash, then he would talk to them about what had happened on Altomare, or he would not have been ashamed to cry and let out his true feelings in front of his so called friends.

'Are they really that stupid for them to think that you belong to them?' Latias was now full blown telepathically laughing at how blind those girls really were.

'Apparently so,' Ash continued, now grinning at how much Latias was laughing. 'Now, back on the topic of Misty,' Ash's voice turned serious for the most part. He still had that look in his eye that made Latias realize how much he bottled up his emotions.

'Misty was following Brock when he came to look for me and both of them are over in the alleyway over there,' Ash pointed over his shoulder at the alleyway that Ash had walked out of minutes before. 'Brock is trying to persuade Misty that it is a really bad idea to interrupt us and she thinks that he is being childish for being afraid of a fourteen year old boy. Personally, I think that Misty should listen to Brock, but what she does is her choice.'

Latias gave a small smile at Ash's expression. He really wanted Misty to come and interrupt them so he could teach her that he belonged to now one.

'So… What are we supposed to do now while Misty is still making her decision?' Latias asked Ash.

He could see the curiosity filling her eyes. 'All that we must do, my dear Tia **(A/N Ash gave Latias a Nickname.)** is wait for Misty to appear, which is in 5…4…3…2…1…Now.'

As Ash finished his statement, Misty came storming out of the alleyway with a look of pure rage on her face. "Ash Ketchum! You better get your butt over here right now or you are in for a world of pain!"

Latias glanced over at Ash and rolled her eyes a bit. If Misty knew what kind of power Ash possessed, she wouldn't even try to threaten Ash.

Ash returned her eye roll and pulled Latias up off of the bench with her hand in his. Misty's cerulean blue eyes widened and she took a step back in shock at the sight of the pair holding hands.

Ash turned, pulling Latias along with him, and started towards a side street closest to the bench they had been sitting on. Misty quickly got over shock and a fire began to burn in her eyes. The only thing, at least for a moment, that kept her from ripping away the "Witch" who was clinging to "her" Ash, was piercing glare that Ash was giving her.

She suddenly had the desire to run away desperately; most likely caused by the aura pulse Ash had sent into the air in an attempt to scare Misty away. Misty just shook it of blaming her nerves on the fact that Ash was giving her a look that she had never seen before on his face.

She began to walk swiftly over to where the pair was, causing Brock to appear from the shadows where he had been watching. But unfortunately for Misty, Brock wasn't fast enough to come to her aid. Not that she really needed any help at the moment.

While Misty had been held in his gaze, Ash and Latias had begun to inch backwards towards the side street. When Ash sensed that Misty was coming towards them again, he turned nudging Latias behind him. Misty saw his eyes flash blue for a moment and the air in front of her suddenly solidified, causing her to fall onto the ground. At that moment, Brock came hurrying into view.

He tried to help Misty, but she pushed him to the side. Brock glanced at Ash and his almost nonexistent eyes widened. In the very depths of Ash's blackish brown eyes, there was a mix of sky blue and cobalt blue, fight for dominance.

'_Huh_,' Brock thought, '_where have I seen this before? It reminds me of Lucario and the colors of his aura… wait… AURA?_'

"Ash! Don't do anything you might regret later."

Ash's head snapped around from the stare of concentration he was giving Misty. Whatever had been holding Misty back suddenly dissolved at the lack of attention it was given.

Brock also saw, along with the wall, the blue fade from Ash's eyes. He returned Brock's stare with no emotion what so ever, on his face or in his eyes. Brock watched as Ash turned and walked away, the girl he was with was following close behind him.

Brock began to move as if he was going to follow Ash, but He turned and gave Brock an icy glare the said "Follow me, and you will regret it for the rest of your life."

Brock felt a cold shiver run through his body as Ash's gaze was turned onto him. He closed his eyes to settle the feeling of fear he felt towards Ash from overwhelming him. When he was finally able to open his eyes again, Ash and the girl were gone and Misty was sobbing quietly on the ground next to him. That was first, Misty, in all the years they had been traveling together, had never cried, not once.

"What did I do wrong," Misty was sobbing so hard Brock could barely understand what she was saying. "Why would choose some random island girl over me. Ash doesn't know anyone on Altomare besides Bianca, Lorenzo, and Latias… Latias?"

As quickly as Misty's crying had started, it stopped. Misty's devastated expression was just as quickly replaced by her absolutely calm one. But her voice shook with hidden rage.

"If that filthy dragon lays one grubby paw on 'my' Ash…" Misty didn't finish the threat she left hanging in the air for all to hear. Brock gulped in fear as he followed Misty back to the pokemon center, trying to calm her down the whole way back.

"Ash will have to come back eventually, so when he does he is going to get the worst beating of his life. Arceus so help me, I'm going to beat the words out of if that is what it takes." Misty muttered under her breath.

Brock rolled his eyes at Misty; she was grumbling threats to herself again. "You do realize," Brock began, "We will have to tell everyone else what happened here today and what happened last time we were here right?"

Misty whirled around at Brock's words; Brock immediately put up is hands in a defensive gesture.

"Why do we have to tell them? They can figure that out themselves." And with her words, Misty began to stomp her way towards the pokemon center. Brock sighed as he watched Misty's retreating form.

**And that concludes the fifth chapter. Again, sorry for taking a while to update. I am in the middle of end of the year testing. Now I want to kill the idiot who invented tests… just kidding. Though, I really do hate testing. Please R&R. **


	6. Chapter 6

What was once here, is now gone a pokemon fanfiction chapter six

**A/N** Hello people of the fanfiction world, again. I am really sorry to all those people who thought I was dead, but as you can see, I'm still alive and writing. I have not been able to update due to the fact that I was testing and school was getting out. So please read and I hope you like it. Thank you to the people who were nice enough to review my last chapter. The reviews are what make me want to keep on typing. Thanks!

"Speech"

'Telepathy'

'_Thoughts'_

With Ash and Latias after they left Brock and Misty,

'Finally,' Ash grumbled to himself more than he was talking to Latias, 'I thought that they would never show up so we could leave.'

Ash didn't really notice in his annoyance at Brock and Misty, but Latias was trailing behind him, lost in thought. Mentally replaying the scene of what had just happened in her mind.

'Ash,' Ash just kept muttering to himself about ungrateful and not trustworthy gym leaders.

'Ash,' Latias repeated. She got the same response as she had gotten before.

'ASH,' she mentally shouted at him. The red and white dragon was tired of being ignored.

He stopped dead in his tracks and slowly turned around at the sound of the angry dragoness.

She sighed in relief; Ash was so oblivious to other things at times.

'Did you really have to be so harsh towards Misty and Brock? Brock was only trying to help you and Misty, was well, trying in her own way to do what she thought was best for you. She just believes that she was the best one for you.'

Latias was shocked to see how emotionless Ash face was. How there was no regret for what he did, how there was no pain at what he made his friends go through.

'Yes Latias, I did have to be that harsh with them.'

'Why? All they ever did was try to do what they thought was best for you?'

'Latias,' Ash wasn't going to tell Latias what he had heard from Misty's thoughts, but it was for the best that he did, or else the energetic dragon was going to find out the hard and painful way.

'If you had been listening to Misty's thoughts when she had confronted us, you would know why I had to do what I did. She was threatening to **kill** anyone so only she could have me. May and Dawn were thinking the same things when we were on the boat coming to the island. They would have hurt you, and I can't let that happen. It goes against what I promised your brother a he was being taken into the Soul Dew, he told me to protect you, and not to let any harm come to you. '

Latias felt a few gentle tears fall down onto her cheek from her brimming eyes. She broke down like thins anytime someone mentioned Latios.

Ash's face softened as he watched Latias softly cry. The pain filled girl reminded Ash of himself when someone or something reminded him of the fallen blue dragon.

On the outside, Latias may have been crying, it was an automatic thing now, but on the inside, she was absolutely shocked. Latias had never had much interaction with the red head when she was on Altomare, but Latias would have never thought that Misty would have transformed from being a sensible, honest and who cared about her friend well being girl to being one with greed and lust for a certain power among her friends type of girl.

Latias felt her whole body tingle as she felt Ash wrap her in a warm and caring embrace. She stiffened; then relaxed into his solid and unmoving body. Ash was her anchor in the world, something that was going to keep her from floating away and from being locked within her sorrow and regrets.

She could feel Ash gently stroking her hair as her sobs began to die down. When Latias finally stopped she looked up to see Ash staring at her with concern clear of his face. His face instantly lit up when he saw that Latias was no longer crying. He took her hand and began to lead her on the route towards the garden.

As soon as Latias began to take the lead, Ash let go of her hand. 'Go on ahead; I'll meet you further up.' Latias nodded at his words and disappeared into a nearby street. Ash watched her walk away and turned around to face a dark corner of the side street he was on.

There was May, standing in said dark corner. At what she thinks of as silent observing, Ash could feel the violent thoughts circulating through the intruders' aura. There was a sudden spike of fear is May's aura as she realized Ash was giving her a glare that would stop even the most horrible member of team rocket dead in their tracks.

May slowly began to retreat back towards the pokemon center. Turning and running when Ash sent a mild pulse of aura into the air to make May move faster, her slow jog/run turned into full out sprinting as Ash increased the aura level in the air. Ash turned; satisfied that May was gone and was going to leave the pair alone long enough that Ash and Latias could not be tracked easily.

He quickly found Latias and tagged her on the shoulder. 'Tag, you're it!'

Latias jumped stifling a squeal, and turned to try and get Ash back for scaring her.

I was going to end the chapter here but I figured it was too short, so enjoy

With May, Max, Dawn, Misty and Brock,

Max and Dawn were lounging around the pokemon center common room waiting for Misty and Brock come back from retrieving Ash, and were waiting for Dawn to come back from her walk so they could get a tour of the city. The doors of the pokemon center burst open as May came sprinting in.

"You..will…never…believe…what…I…just…saw!" May managed to gasp out as she stood in front of the pair panting heavily.

"Geez May! What have you been doing? Running a marathon?" Came the irritating voice of May's younger brother Max, as he mocked her for being out of shape.

May just rolled her eyes and rapidly told the pair on what she had seen and heard on her walk around the town. Every so often May would glance over her shoulder to make sure that Misty and Brock were not coming in the doors. When she was finished, everything between the trio was silent as Max and Dawn processed the information. If Ash had been there with them he would have felt the killing intent in Dawn's aura at what she was hearing about Latias.

Finally Max worked up the courage to ask a vital question that none of them knew the answer to, "So what really happened when Misty, Brock, and Ash were here last time? And besides, that Latias that Misty was talking about couldn't have been the legendary…right? Ash just really had some dumb luck when he saw all those other legendaries in the other regions. It was the same dumb luck that got him through all of the leagues."

Both May and Dawn shook their head, the y really had no idea what had happened when Misty, Brock and Ash were here the last time. Neither Misty nor Brock had told them the story and as they know, Ash had flat out refused to speak a word ever since it happened. As they came to the end of this thought, the pokemon center door burst open once more. It was Misty and Brock.

Most likely they were there only because Brock managed to calm Misty down for the time being. Ash was nowhere to be seen, not that they were surprised after what May had seen and heard. The duo was instantly surrounded the pair while rapidly firing question after question at them.

"What happened," "Where's Ash," and, "What happened last time you were on the island?" Misty had managed to keep her cool until someone, most likely Max, asked the last question. What happened last time you were on the island? Misty snapped.

"Hmm, let me thing about that for a moment. I know! Try asking Ash next time you seen him. I'm sure he would love to speak to you about it. Maybe he'll open up to you since this is one of the places Ash loves most in the world."

Misty smirked at them evilly, already knowing that Ash wasn't going to tell them a thing. They all watched, with their mouths hanging open, as Misty stormed into her room and slammed it for the night.

**A/N **Thank you for reading my new chapter. Please remember to click that little blur button at the bottom of the screen that says review this chapter. And I promise that the chapters will be hopefully coming in faster because schools out. Until next time,

Electricprincess889


	7. Chapter 7

What was once here, is now gone

A Pokémon Fanfiction

Chapter seven

Disclaimer: I only own my computer… Nothing else. *Sniffs sadly*

Back with Ash and Latias at the Garden of the Lati...

The pair came shimmered into existence at the very entrance of the garden. Latias somewhat happy look that she had on her face vanished as she began to recall all the happy times she and her brother had spent just sitting around in the treetops, talking like nothing was ever going to happen to either one of the. At least not for a very long time. Legendries had very long lifespans. They are able to die, but only under very extreme circumstances. Like all of your energy being drained rapidly out of your body. Like what happened to Latios.

Ash, well... he managed to have absolutely no emotion on his face. But you could see the deep sadness and hurt in the very depths of his eyes. As the two approached the fountain that held the Soul Dew, Ash could visibly see the pain and suffering on Latias face. He stopped and turned to fully face the suffering dragoness, 'Latias… You don't need to come with me… I can do this by myself.'

You could see the relief in Latias' facial features. She nodded and motioned for Ash to continue on without her. Latias then retreated to the tree where she and Latios used to sleep at night.

Ash watched her go, with worry, sadness and something else in his eyes? He shook his head in obvious distress and continued to walk towards the fountain. As he gazed down at the shimmering jewel, Ash let a few tears to escape his eyes.

'I'm so sorry Latios. If I had never come to the garden in the first place, then you would still be alive today….. It would have been better if I never had come to Altomare and stayed away.'

The tears began to flow faster as the barriers he had put up for so many years came crumbling down. The silence that had descended over the garden was broken when Latias gave a sudden squeal of surprise and pain. Ash whirled around and came upon the sight of Bianca pinning Latias down with her hands behind her back. The girl was yelling at a confused Ash while twisting Latias' hands into a more controlling position.

"I told you to stay away Ketchum! It's all your fault that Latios is dead! If you had never come to Altomare, Latios would still be alive! You know what? The whole world would have been better off without you in it!" By the time Bianca was done yelling at Ash, she had Latias on her feet and was walking backwards towards the entrance of the garden.

This wasn't what Ash wanted, all he wanted to do was say he was sorry to his lost friend and mourn Latios by himself. And when he looked at Latias, he could see that she felt the same. But Ash also knew that he had to stay in control of his emotions. It could severely injure or even kill Bianca. But more importantly, Latias was in the way.

Ash gently encased Latias in a small bubble of aura and lifted her towards him. When she was safely at his side, he popped the bubble and gave her a swift hug and a kiss on the cheek before turning to Bianca. The girl turn to look Ash bravely in the eye and… Well to say the least, she failed... Miserably. As soon as she looked into Ash's aura filled eyes, she had to look away in pure terror at what she saw. Ash was no longer the carefree, happy-go-lucky trainer he once was. He had seen more things then she would and could never imagine.

While Ash was about to deal with Bianca, Latias was at his side, blushing. She had always liked Ash, but never expected him to feel something for her. One of her new abilities was to be able to feel the emotions of others. But so far she could only feel the really strong ones. The paralyzing fear or unconditional love. She was beginning to feel something coming from deep within Ash's heart. Not just the sadness and pain he had for anyone he had let down in some way.

Ash was about to try something that he had never been able to test before. He slowly began to use his aura to slowly break through the barriers of Bianca's mind. And he was completely shocked at what he found. Bianca had been just as hurt as he was when Latios died. But for a very different reason, not because she had grown up with him and loved him like a brother. But because she loved him, as in full blown head over heels in love with the blue and white Lati. That was part of the reason why she had blown up at Ash, but Ash was not mad about that part. He to felt that it was his fault that Latios was now dead. After all, had he not come into the garden, those cameras would not have tracked him, therefore not discovered the garden in the first place.

As Ash withdrew his aura from Bianca's mind, he began to have a new outlook on the happenings on Altomare. He began to realize how the whole city had suffered, but at the same time prospered into a new kind of city. One that didn't take as many things for granted as they did before. Bianca was crying as she had to revisit the memories she had locked away for so long. Latias was crying as well, for the sake of her brother, Bianca, Ash and herself. What Bianca didn't know was that Latios had returned her feelings. Latias could sense this every time she and Bianca would talk to the Soul Dew.

When Bianca looked up at Ash again, she didn't have to look away as she had to do before. The level of his gaze had gone down, a lot. She could look into his black and blue eyes without flinching or fearing that he was going to lose control and harm her. She slowly began to understand how he had felt all of these years, with no one to help him through his pain. And as Bianca began to approach Latias, the only movement Ash made was to go back to standing at the fountain.

Latias turned her big amber eyes upon Bianca. She too understood why Bianca had been acting like she had been this morning. They stood in front of each other, neither saying a word. And as if a gate had been opened the tears began to pour out as they sprang forward to hug. All past differences forgiven.


	8. Chapter 8

What was once here, is now gone chapter eight

A pokemon fanfiction

Disclaimer: I don't own anything but my computer...*Sniffs*

A gentle breeze moved through the garden, and the Soul Dew glowed even brighter than it already did. A small smile came upon Ash's face. He whispered one more thing to his lost friend,

"Thank you for giving me a second chance."

By the time he had turned around to see what Bianca and Latias were doing, Bianca had already left after apologizing to Latias and to Ash. Latias had joined Ash at the fountain and now had her hand in his hand and was giving him a gentle smile. Telling him it was not his fault that Latios died. He made his choice, as did she.

Ash smiled back and gently pulled Latias towards the garden entrance. They were about to reach the exit when and ice beam suddenly froze the ground in front of them. Ash immediately pulled Latias behind him. Since she was a dragon type, the ice type attack would harm her more than him if she was hit.

Right after the ice beam hit the ground, another one hit Ash. Who happened to be right where Latias had been standing moments before. Thankfully, when he was training to use his aura, part of his training was to be able to withstand any type of attack. Whether is to a physical pokemon or human, or a mental attack. He was able to shrug it off and started to look for the attacker.

As the dust cleared, Ash and Latias were able to see who had intruded the Lati's sanctuary. It was Misty, May and Dawn with all of their ice and water type pokemon standing in front of them. They glared at Latias with such an icy intensity, Giritina was wondering why the Distortion world was starting to freeze, **(Get it? Because people thought that it was hell? Hell freezing over? You know what. Forget it, never mind. You people have no sense of humor)**.

There were three simultaneous cries of 'Ice beam,, Ice shard and Blizzard' All sent at once in Latias direction. The pair was obscured from view and the ice attacks just kept coming. Then one voice could be heard above all the rest, "Glaceon! Shadow Ball!"

Several of the deep black and purple balls flew into the barrage of ice attacks, effectively creating an explosion that could be felt throughout the entire city. The attacks stopped as the smoke and dirt started to clear away. What the three girls saw next shocked them to their very core.

Ash and Latias stood unharmed exactly where they had been last standing. Latias still looked in shock at how she was attempted to be seriously injured. Ash on the other hand, was livid. There was a mask of deadly fury on his face and his eyes weren't just flashing blue this time. They were full on sea blue-green. That was a sure sign someone had to pay.

The garden had been previously filled with the sounds of other bird and bug type pokemon. Now it had gone a deathly silent noise. All you could hear was the slight panting of Misty, May and Dawn's pokemon. But even they went silent as they began to feel the waves of power coming off of Ash. Ash had always had that type of feel around him. That you didn't want to mess with him and it commanded respect. Though people didn't really notice it until after Ash had trained that brief amount of time with Lucario.

Ash was exuding so much power it was visible. That was another sign that an aura user was starting to lose control over what they were doing. Ash was very good at controlling his temper. Much better than people thought he was. Insult him, whatever. Insult his skills; people can have their own opinions. But insult his pokemon or family or friends, you might want to be near somewhere close to where you can get immediate medical attention. But try to harm Latias, prepare to face an almost uncontrollable, highly dangerous aura user.

The girls brought out their strongest pokemon and prepared to try and stand up against Ash. All the while slowly inching backwards from the ticking time bomb known as their seemingly best friend. Misty had out her Gyrados, Dawn had out her Piplup and May had out her Blaziken.

Ash released a pokemon that the girls had never seen before. It was about the size of Piplup and Pikachu. Though you could also feel a euphoric feeling fill the air. It felt like the girls could win anything, do anything, be anyone they wanted to be. And no matter what would happen they would win. It was radiating out from the small pokemon. The three began to relax to the point that they were almost asleep.

The enraged aura user came no visible command, but you could feel the atmosphere in the garden change. A blue light surrounded all three of the pokemon. Nothing happened to them at first but then they were back with a loud bang into a large tree. The three pokemon had barley anytime to recover before the v-shaped crest on the top of the Pokémon's head began to glow with a soft green light. Sunlight began to swirl down towards the pokemon in the fading sunlight. A powerful beam shot towards the three down on the ground pokemon.

There would have been a resounding explosion if someone had not interfered. A tall serpent like creature stood in front of pokemon, and a green barrier sprung out from it. Causing the beam to rebound in several different directions. As the dust cleared, the serpent became clearer. It had a very long and thin body, tan and ending in a rainbow fan-like tail. The crests on the side of its head were the same rainbow pattern. Ash, if he could any more, tensed at the new figure that had accompanied the snake.

"Now, now Ash," The voice chided, "Is that any way to treat a friend?"

Ash only stood there, as the smoke revealed a tall blonde haired woman in black. Cynthia smiled and began to walk towards Ash. She got within five feet of him when she bounced off of an invisible wall that glowed blue faintly before returning to being invisible. Cynthia then brought out her Lucario to break through the aura barrier, but Ash was already gone, as was Latias and the small pokemon that Ash had.

**Hello people of the fanfiction world and whoever reads this story. Hope you liked the chapter. And I'm sorry for not getting it up sooner but I was busy with school starting back in September and other times I was just being lazy. ;) So please review and tell me what you think. And from last chapter, I got lots of reviews about when I was starting the romance part of the story. Well there was the first part of it. I'm not very good at the love stuff, but I try my hardest. Review and you can PM me if you have any questions. **


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